Contacts of the strand formed by residues 112 - 126 (chain A) in PDB entry 1TNF
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A GLY* 2.6 30.0 + - - +
104A GLU* 5.0 2.5 - - + -
109A ALA 5.3 3.8 - - - +
110A GLU 2.9 15.2 + - - +
111A ALA* 1.3 73.3 - - - +
113A PRO* 1.3 67.1 - - + +
72C THR 5.5 1.4 - - - -
73C HIS* 3.2 36.5 + - + +
101C CYS 2.9 22.5 + - - -
102C GLN* 3.4 39.0 + - - +
103C ARG* 3.9 27.0 - - + +
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Residues in contact with PRO 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLY 3.3 11.0 - - - +
67A GLN* 3.7 13.4 - - + +
111A ALA 4.4 1.6 - - - +
112A LYS* 1.3 88.3 - - + +
114A TRP* 1.3 59.4 + - - +
115A TYR* 4.5 24.5 - - + +
73C HIS* 2.9 50.7 + - + +
75C LEU* 5.8 2.5 - - + -
99C SER* 3.8 1.7 + - - -
102C GLN* 4.6 2.4 + - - -
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Residues in contact with TRP 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PHE* 3.9 13.7 - - + -
65A LYS* 3.1 29.8 - - - +
66A GLY* 2.7 39.8 + - - +
68A GLY 3.1 31.5 + - - -
69A CYS* 3.3 27.5 - - - -
70A PRO* 5.8 0.7 - - + -
74A VAL* 5.4 1.3 - - + -
76A LEU* 4.2 5.6 - - + -
100A PRO* 3.9 34.1 - - + -
101A CYS* 5.1 3.1 - - + +
112A LYS 4.7 0.9 - - - -
113A PRO* 1.3 73.7 - - - +
115A TYR* 1.3 69.1 + - - +
116A GLU* 4.2 8.5 - - + -
141A TYR* 3.5 44.0 - + + -
99C SER* 4.4 9.0 - - - +
102C GLN* 4.9 8.5 - - + +
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Residues in contact with TYR 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 6.5 0.2 - - + -
64A PHE 3.0 7.0 - - - +
65A LYS* 3.7 21.1 - - + -
113A PRO* 4.5 26.7 - - + +
114A TRP* 1.3 75.5 - - - +
116A GLU* 1.3 68.8 + - - +
117A PRO* 3.9 0.2 - - - +
143A LEU* 3.7 21.8 - - + -
146A GLU* 5.3 0.2 - - - -
75C LEU* 3.7 27.9 - - + +
97C ILE* 3.5 64.7 - - + +
98C LYS* 3.8 9.8 - - - +
99C SER* 4.0 12.3 + - - -
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Residues in contact with GLU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU* 3.5 2.1 - - - -
64A PHE* 2.7 46.3 + - + +
76A LEU* 4.4 12.3 - - + -
98A LYS* 3.4 39.5 + - + +
99A SER 3.1 21.4 - - - +
100A PRO* 4.0 26.5 - - + +
114A TRP* 4.2 6.1 - - + -
115A TYR* 1.3 77.3 - - - +
117A PRO* 1.3 66.5 - - - +
118A ILE* 5.3 0.4 - - + -
116B GLU* 5.2 2.3 - - - +
98C LYS* 4.1 10.2 - - - +
99C SER 5.8 0.2 + - - -
116C GLU* 5.4 0.9 - - - +
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Residues in contact with PRO 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLN* 4.8 3.8 - - - +
62A VAL 3.6 5.4 - - - +
63A LEU* 3.6 21.5 - - + -
98A LYS* 3.0 20.1 + - - +
115A TYR 3.9 0.9 - - - +
116A GLU* 1.3 83.3 - - - +
118A ILE* 1.3 60.9 + - - +
119A TYR* 4.0 1.8 + - + +
96C ALA* 3.9 18.6 - - + -
97C ILE 3.5 20.4 - - - +
98C LYS* 3.8 32.9 + - + +
118C ILE* 5.0 5.2 - - + -
119C TYR 6.1 0.9 - - - +
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Residues in contact with ILE 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A SER 4.1 0.2 - - - +
61A GLN* 3.3 3.7 - - - +
62A VAL* 2.8 42.3 + - + +
64A PHE* 4.0 21.5 - - + -
76A LEU 4.3 4.5 - - - +
78A HIS* 3.7 34.3 + - + +
96A ALA* 3.6 33.4 - - + +
98A LYS* 3.8 35.2 - - + +
116A GLU 3.8 1.4 + - - +
117A PRO* 1.3 76.5 - - - +
119A TYR* 1.3 64.0 + - - +
120A LEU* 3.9 8.3 - - + -
117B PRO* 5.6 4.0 - - + -
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Residues in contact with TYR 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A TYR* 3.4 15.9 - - + +
60A SER* 3.1 32.5 - - - -
61A GLN* 3.6 18.4 - - + -
78A HIS* 5.2 0.2 - - - -
96A ALA* 5.3 0.2 - - - +
117A PRO* 4.0 2.0 + - + -
118A ILE* 1.3 77.5 - - - +
120A LEU* 1.3 84.8 + - - +
121A GLY* 5.3 1.6 - - - -
151A TYR* 4.2 3.4 - + - -
61B GLN* 3.9 7.6 + - - -
119B TYR* 4.5 25.7 - + + +
57C LEU* 5.4 3.5 - - - +
119C TYR* 3.5 50.0 - + + +
121C GLY* 3.3 39.9 + - - -
122C GLY 4.1 0.3 + - - -
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Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TYR* 3.2 1.9 - - - -
60A SER 2.8 30.9 + - - +
78A HIS* 3.0 37.0 - - - +
80A ILE* 4.1 18.2 - - + -
94A LEU* 3.6 37.5 - - + +
95A SER 3.9 2.9 - - - +
96A ALA* 3.7 22.2 - - + -
118A ILE* 3.9 6.7 - - + -
119A TYR* 1.3 98.4 - - - +
121A GLY* 1.3 57.5 + - - +
61B GLN* 3.5 19.3 - - - +
119B TYR* 4.4 4.9 - - - -
151B TYR* 4.3 4.3 - - - +
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Residues in contact with GLY 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A LEU* 5.1 3.8 - - - -
58A ILE 2.9 15.7 - - - -
59A TYR* 3.8 4.7 - - - -
94A LEU* 3.6 11.5 - - - +
119A TYR* 5.3 1.3 - - - -
120A LEU* 1.3 76.3 - - - +
122A GLY* 1.3 56.8 + - - -
59B TYR* 3.7 0.3 - - - -
119B TYR* 2.8 32.4 + - - -
151B TYR* 3.5 15.4 + - - -
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Residues in contact with GLY 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 4.6 6.5 - - - +
58A ILE 2.9 25.5 + - - +
94A LEU* 3.8 6.5 - - - +
121A GLY* 1.3 73.6 - - - -
123A VAL* 1.3 62.3 + - - -
124A PHE* 3.3 25.3 + - - -
59B TYR* 3.5 18.4 - - - -
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Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LEU* 3.8 29.4 - - + -
56A TYR 3.4 13.7 - - - +
57A LEU* 4.3 16.8 - - + -
122A GLY* 1.3 73.2 - - - -
124A PHE* 1.3 67.1 + - - +
157A LEU* 4.3 5.4 - - + -
13B VAL* 4.3 14.1 - - + -
14B ALA 5.2 1.1 - - - +
15B HIS* 3.7 24.3 - - - +
36B LEU* 4.0 4.5 - - - +
57B LEU* 4.8 0.9 - - + -
59B TYR* 2.8 25.3 + - + +
155B ILE* 3.8 34.1 - - + -
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Residues in contact with PHE 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LEU* 3.1 7.3 - - - -
56A TYR* 2.9 30.9 + - - +
58A ILE* 3.5 26.7 - - + -
82A ARG* 5.9 0.7 - - - +
93A LEU* 3.5 47.6 - - + -
94A LEU* 3.9 22.4 - - + -
122A GLY* 3.3 24.5 - - - -
123A VAL* 1.3 74.6 - - - +
125A GLN* 1.3 60.2 + - - +
126A LEU* 3.6 10.3 + - + -
15B HIS* 3.3 36.3 - + - -
34B ASN* 3.6 25.4 - - + +
36B LEU* 4.3 4.0 - - - -
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Residues in contact with GLN 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A GLU* 3.9 19.9 + - + +
54A GLY* 3.3 10.8 - - - +
55A LEU* 3.5 20.0 - - + -
82A ARG* 4.2 13.0 + - - -
124A PHE* 1.3 71.8 - - - +
126A LEU* 1.3 68.9 + - - +
127A GLU* 4.3 13.8 + - - +
8B PRO* 6.1 8.5 - - + -
36B LEU* 3.6 27.5 - - + +
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Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A VAL* 4.0 11.4 - - + -
52A SER 4.3 2.5 - - - -
53A GLU* 3.6 6.8 - - - +
54A GLY 2.9 25.4 + - - -
56A TYR* 3.7 33.7 - - + -
58A ILE* 3.7 28.7 - - + -
82A ARG* 3.3 42.0 - - - +
93A LEU* 5.0 0.4 - - + -
124A PHE* 3.6 6.9 + - + +
125A GLN* 1.3 79.9 + - - +
127A GLU* 1.3 61.8 + - - +
130A ASP* 3.3 11.4 - - - +
132A LEU* 3.9 20.0 - - + -
154A ILE* 5.2 2.7 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il